Choosing Intel MKL BLAS when compiling R
Jonathan: Compiling R, and linking to Intel MKL, is quite simple, as long as you are using a recent version of MKL. Intel has a MKL Link Advisor at http://software.intel.com/en-us/articles/intel-mkl-link-line-advisor/ Choose the linking model you want, and then use the --with-blas option on configure. For example, on my Mac, to link dynamically with the parallel version (which can be controlled with environment variables), I use the following: '--with-blas=-L$(MKLROOT)/lib -lmkl_rt -lpthread -liomp5' I compiled R 2.14.0 this morning with this option, and it seems to work fine. I'm not sure what Dirk was referencing about how MKL is no longer compatible with R. If there is an issue, it would be good to know about it. Perhaps he can point us to the page in the documentation where this is mentioned. I hope this helps. Michael
On Nov 1, 2011, at 7:59 PM, <r-sig-hpc-request at r-project.org> <r-sig-hpc-request at r-project.org> wrote:
Message: 1
Date: Tue, 1 Nov 2011 14:36:50 -0700
From: Jonathan Greenberg <jgrn at illinois.edu>
To: r-sig-hpc at r-project.org
Subject: [R-sig-hpc] Choosing Intel MKL BLAS when compiling R
Message-ID:
<CABG0rfvnoswR+Hi7peaTAPczT_4j6FTV-H0rDLwqJOw05HrLuw at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
r-sig-hpc'ers:
I am compiling R 2.14 from scratch on a cluster computer (I can't use
any package managers for the install, unfortunately), and they have
the Intel MKL libraries available for BLAS/LAPACK. I have not
successfully gotten a configure/make/make install combo yet that uses
multiple CPUs to do, say:
a = matrix(rnorm(5000*5000), 5000, 5000)
b = matrix(rnorm(5000*5000), 5000, 5000)
# This following line, minimally, should be getting distributed.
c = a%*%b
First off, I've tried compiling it with the configure flags:
./configure --prefix=/myprefix/ --enable-BLAS-shlib
How do I then select the Intel MKL libraries to be used as the BLAS?
They are located in /usr/local/intel-11.1/mkl/lib/em64t
Thanks!
--j
--
Jonathan A. Greenberg, PhD
Assistant Professor
Department of Geography
University of Illinois at Urbana-Champaign
607 South Mathews Avenue, MC 150
Urbana, IL 61801
Phone: 415-763-5476
AIM: jgrn307, MSN: jgrn307 at hotmail.com, Gchat: jgrn307, Skype: jgrn3007
http://www.geog.illinois.edu/people/JonathanGreenberg.html
------------------------------------------- Michael Braun Associate Professor of Management Science (Marketing Group) MIT Sloan School of Management 100 Main St.., E62-535 Cambridge, MA 02139 braunm at mit.edu 617-253-3436 -------------- next part -------------- An HTML attachment was scrubbed... URL: <https://stat.ethz.ch/pipermail/r-sig-hpc/attachments/20111101/8120ed31/attachment.html> -------------- next part -------------- A non-text attachment was scrubbed... Name: smime.p7s Type: application/pkcs7-signature Size: 1844 bytes Desc: not available URL: <https://stat.ethz.ch/pipermail/r-sig-hpc/attachments/20111101/8120ed31/attachment.bin>